GROMACS¶

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

Useful Links¶

Using GROMACS on Cirrus¶

GROMACS is Open Source software and is freely available to all Cirrus users. The central installation supports the single-precision version of GROMACS compiled with MPI and OpenMP support.

GROMACS is installed centrally on Cirrus as a module via Spack. To obtain information on which versions are available use, e.g.,

module avail gromacs
...
   gromacs/2025.2 (D)

The gmx_mpi binary is available after loading a gromacs module. To see details of the build one can use, e.g.,

module load gromacs
gmx_mpi -version

This should show that GROMACS is compiled with the GNU Compiler Collection, along with other compile-time information.

Running GROMACS jobs¶

GROMACS can use full nodes in parallel (with the --exclusive option to sbatch) for larger problem sizes, or run in parallel (or even serial) on a subset of the cores on a node if the problem size is smaller.

For general information on running SLURM jobs, see Running jobs on Cirrus.

Example: an exclusive GROMACS job¶

The following script will run a GROMACS MD job using 2 nodes (576 cores) with MPI only (OMP_NUM_THREADS=1).

Exclusive SLURM job submission for GROMACS (MPI)

#!/bin/bash

#SBATCH --time=00:20:00
#SBATCH --export=none

#SBATCH --exclusive
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=288
#SBATCH --cpus-per-task=1

#SBATCH --partition=standard
#SBATCH --qos=short

#SBATCH --distribution=block:block
#SBATCH --hint=nomultithread

module load PrgEnv-gnu
module load gromacs

export OMP_NUM_THREADS=1

srun gmx_mpi mdrun -s problem-initial-condition.tpr

Example: a hybrid MPI/OpenMP job¶

The following SLURM submission will run a GROMACS MD job using 2 nodes with 48 MPI processes per node (96 MPI processes in total), and 6 OpenMP threads per MPI process (576 cores in total). Gromacs typically recommends between 1 and 8 OpenMP threads per MPI process.

Exclusive SLURM job submission for GROMACS (hybrid OpenMP/MPI)

#!/bin/bash

#SBATCH --time=00:20:00
#SBATCH --export=none

#SBATCH --exclusive
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=48
#SBATCH --cpus-per-task=6

#SBATCH --partition=standard
#SBATCH --qos=short

#SBATCH --distribution=block:block
#SBATCH --hint=nomultithread

module load PrgEnv-gnu
module load gromacs

export OMP_NUM_THREADS=6
export OMP_PLACES=cores

srun gmx_mpi mdrun -s problem-initial-condition.tpr

Example: a non-exclusive job¶

GROMACS can run on a subset of cores in a node. The following script will run a GROMACS MD job using 36 cores on a single node.

Non-exclusive SLURM job submission for GROMACS (MPI)

#!/bin/bash

#SBATCH --time=00:20:00
#SBATCH --export=none

#SBATCH --ntasks=36
#SBATCH --cpus-per-task=1

#SBATCH --partition=standard
#SBATCH --qos=short

#SBATCH --distribution=block:block
#SBATCH --hint=nomultithread

module load PrgEnv-gnu
module load gromacs

export OMP_NUM_THREADS=1

srun gmx_mpi mdrun -s problem-initial-condition.tpr

You may need to add a budget code to the above examples

#SBATCH --account=<code>

using the relevant project budget code.

Warning message¶

The warning message

[CRAYBLAS_WARNING] Application linked against multiple cray-libsci libraries

may appear in the standard error channel when running the centrally installed version. The warning is benign and may be ignored.

Compiling Gromacs¶

If you require a version of GROMACS which is not available via a central module, other versions may be installed via Spack. For information us, e.g.,

module load spack
spack info gromacs

See using Spack on Cirrus for further information on Spack.